The Santa Fe River is unusual in that it completely disappears underground and then reappears 3 miles (4.8 km) downstream. The river drops into a large sinkhole in O'Leno State Park and reappears in the adjacent River Rise Preserve State Park. A map of the watershed clearly shows the gap in the river where it flows underground.[3] Springs like Gilchrist Blue, Ginnie, Hornsby, Lily, Poe, and Rum Island springs are located at the banks of the river, mostly downstream of the river's reappearance above ground level.[4]

The water temperature near the numerous springs is always around 72 °F (22 °C).[5] The area is sparsely populated compared to the rest of Florida, there have been sightings of animals like the black bear, bobcat, the rare Florida panther and due to the near-constant water temperatures along many portions of the river, manatees.[6] As with many rivers in Florida, plant and animal fossil remnants are plentiful along the Santa Fe.[7][8][9]